This follows up on a thread this past July [1] that never reached a clear conclusion as we ended up discussing ways of synchronizing multiple animations since display:none can be used for that purpose in Webkit.
One could say that display and animation properties are orthogonal to one another i.e. the latter animates properties, the latter what kind of box an element generates. So animations on a display:none element are run so that querying the animated properties along the way will return the expected values; and the visual result of turning the element back to display != none would reflect the current state of the animation. This would be true for the animated children of a display:none parent, as well as for visibility:hidden elements and their children.
This would also be consistent with what would happen if your animation was entirely script-based with no use of CSS3 Animations.
Besides the implementation/runtime cost of managing invisible animations, what are the issues with this model ?
[1] http://lists.w3.org/Archives/Public/www-style/2011Jul/0267.html